3dkt

Crystal structure of Thermotoga maritima encapsulin

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Maritimacin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 120	Putative uncharacterized protein × 60 （Q9WZP3） water × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MARIT_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 1–265 Author chain B； PDBConstruct 1–265； UniProt 1–265 Author chain C； PDBConstruct 1–265； UniProt 1–265 Author chain D； PDBConstruct 1–265； UniProt 1–265 Author chain E； PDBConstruct 1–265； UniProt 1–265 Author chain F； PDBConstruct 1–265； UniProt 1–265 Author chain G； PDBConstruct 1–265； UniProt 1–265 Author chain H； PDBConstruct 1–265； UniProt 1–265 Author chain I； PDBConstruct 1–265； UniProt 1–265 Author chain J； PDBConstruct 1–265； UniProt 1–265

Putative uncharacterized protein

OrganismNot specified

UniProt Q9WZP3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 120	Maritimacin × 60 （Q9WZP2） water × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WZP3_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain K； PDBConstruct 1–8； UniProt 106–113 Author chain L； PDBConstruct 1–8； UniProt 106–113 Author chain M； PDBConstruct 1–8； UniProt 106–113 Author chain N； PDBConstruct 1–8； UniProt 106–113 Author chain O； PDBConstruct 1–8； UniProt 106–113 Author chain P； PDBConstruct 1–8； UniProt 106–113 Author chain Q； PDBConstruct 1–8； UniProt 106–113 Author chain R； PDBConstruct 1–8； UniProt 106–113 Author chain S； PDBConstruct 1–8； UniProt 106–113 Author chain T； PDBConstruct 1–8； UniProt 106–113

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3dkt
Deposition date deposition_date	2008-06-26
Structure title title	Crystal structure of Thermotoga maritima encapsulin
Keywords keywords	;enzyme encapsulation, nanocompartment, oxidative stress, ferritin-like protein, hk97-fold, Antibiotic, Antimicrobial, Bacteriocin, Cobalt, Hydrolase, Protease, Secreted, STRUCTURAL PROTEIN-VIRUS LIKE PARTICLE COMPLEX ;; STRUCTURAL PROTEIN/VIRUS LIKE PARTICLE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3dkt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dkt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dkt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	0.00 Å
Rg (electron density)	102.50 Å
Total Rg	102.70 Å
Atom count	131820
Residues	16320
Excluded volume	2360400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dkt__assembly_1__model_1`	120-meric （120）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Maritimacin
Molecular weight formula_weight	30516.8 kDa
EC 编号 ec_number	3.4.-.-
Source method src_method	nat
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	22070

MEFLKRSFAPLTEKQWQEIDNRAREIFKTQLYGRKFVDVEGPYGWEYAAHPLGEVEVLSDENEVVKWGLRKSLPLIELRATFTLDLWELDNLERGKPNVDLSSLEETVRKVAEFEDEVIFRGCEKSGVKGLLSFEERKIECGSTPKDLLEAIVRALSIFSKDGIEGPYTLVINTDRWINFLKEEAGHYPLEKRVEECLRGGKIITTPRIEDALVVSERGGDFKLILGQDLSIGYEDREKDAVRLFITETFTFQVVNPEALILLKF

Entity 2 Entity 2 polymer

Description description	Putative uncharacterized protein
Molecular weight formula_weight	816.9 kDa
Source method src_method	nat
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,L,M,N,O,P,Q,R,S,T

GGDLGIRK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id	3dktA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

Domain ID domain_id	3dktJ01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2400 — Major capsid protein gp5 fold
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3dktJ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily	10 — hypothetical protein PF0899 domain

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Unit-cell length a length_a	669.040 Å
Unit-cell length b length_b	669.040 Å
Unit-cell length c length_c	669.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	960

Space group space_group	F 41 3 2
Space-group number int_tables_number	210
Crystal system crystal_system	—

Resolution resolution	3.104 Å
Low-resolution limit resolution_low	49.867 Å
R factor r_factor	0.2200
R_work r_work	0.2190
R_free r_free	0.2390

Crystal structure of Thermotoga maritima encapsulin

1. Protein Identity and Related Structures Protein Identity & Related Structures

Maritimacin

State in the Current Structure

Other States of the Same Protein in the Database

Putative uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dkt__assembly_1__model_1

3dkt__assembly_1__model_1 | I(q)

3dkt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)

Crystal structure of Thermotoga maritima encapsulin

1. Protein Identity and Related Structures Protein Identity & Related Structures

Maritimacin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dkt__assembly_1__model_1

3dkt__assembly_1__model_1 | I(q)

3dkt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)